Wait wait wait, I was thinking an alternate story.
I'll take it shortly, we'll be playing two characters each, as our main characters. Basically, I will be the Mary type character, and maybe the person who gets her into the Dan (or someone else significant). I will start out with the Mary chara telling a story and referring back to my other character who I then start playing.
Your first, is telling the same story as the Mary chara does, but as the Kuroha chara who created the havoc. He has just done the worst things and thinks back to the Shintaro-like chara, who you then start playing as your main. Get it?